source: trunk/src/series/civ2vel_3C.m @ 1147

Last change on this file since 1147 was 1144, checked in by sommeria, 5 months ago

false flags modified in civ_series with new conventions, low pass filter adde to transform_field

File size: 22.9 KB
Line 
1%'civ2vel_3C': combine velocity fields from two cameras to get three velocity components
2%------------------------------------------------------------------------
3% function ParamOut=civ2vel_3C(Param)
4%
5%OUTPUT
6% ParamOut: sets options in the GUI series.fig needed for the function
7%
8%INPUT:
9% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
10% In batch mode, Param is the name of the corresponding xml file containing the same information
11% when Param.Action.RUN=0 (as activated when the current Action is selected
12% in series), the function ouput paramOut set the activation of the needed GUI elements
13%
14% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
15% see the current structure Param)
16%    .InputTable: cell of input file names, (several lines for multiple input)
17%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
18%    .OutputSubDir: name of the subdirectory for data outputs
19%    .OutputDirExt: directory extension for data outputs
20%    .Action: .ActionName: name of the current activated function
21%             .ActionPath:   path of the current activated function
22%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
23%             .RUN =0 for GUI input, =1 for function activation
24%             .RunMode='local','background', 'cluster': type of function  use
25%             
26%    .IndexRange: set the file or frame indices on which the action must be performed
27%    .InputFields: sub structure describing the input fields withfields
28%              .FieldName: name(s) of the field
29%              .VelType: velocity type
30%              .FieldName_1: name of the second field in case of two input series
31%              .VelType_1: velocity type of the second field in case of two input series
32%              .Coord_y: name of y coordinate variable
33%              .Coord_x: name of x coordinate variable'
34
35%=======================================================================
36% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
37%   http://www.legi.grenoble-inp.fr
38%   Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr
39%
40%     This file is part of the toolbox UVMAT.
41%
42%     UVMAT is free software; you can redistribute it and/or modify
43%     it under the terms of the GNU General Public License as published
44%     by the Free Software Foundation; either version 2 of the license,
45%     or (at your option) any later version.
46%
47%     UVMAT is distributed in the hope that it will be useful,
48%     but WITHOUT ANY WARRANTY; without even the implied warranty of
49%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
50%     GNU General Public License (see LICENSE.txt) for more details.
51%=======================================================================
52
53function ParamOut=civ2vel_3C(Param)
54disp('test')
55%% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed
56if isstruct(Param) && isequal(Param.Action.RUN,0)
57    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
58    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
59    ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
60    ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
61    ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
62    ParamOut.FieldTransform = 'off';%use the phys  transform function without choice
63    %ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only)
64    ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',
65    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
66    ParamOut.OutputDirExt='.vel3C';%set the output dir extension
67    ParamOut.OutputSubDirMode='two'; % the two first input lines are used to define the output subfolder
68    ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
69    %check the input files
70    ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
71    first_j=[];
72    if size(Param.InputTable,1)<2
73        msgbox_uvmat('WARNING',['two or three input file series are needed'])
74    end
75    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
76    PairString='';
77    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
78    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
79    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
80        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
81    if ~exist(FirstFileName,'file')
82        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
83    elseif isequal(size(Param.InputTable,1),1) && ~isfield(Param,'ProjObject')
84        msgbox_uvmat('WARNING','You may need a projection object of type plane for merge_proj')
85    end
86    return
87end
88
89%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
90ParamOut=[]; %default output
91%% read input parameters from an xml file if input is a file name (batch mode)
92checkrun=1;
93if ischar(Param)
94    Param=xml2struct(Param);% read Param as input file (batch case)
95    checkrun=0;
96end
97hseries=findobj(allchild(0),'Tag','series');
98RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
99WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
100
101
102%% root input file(s) name, type and index series
103RootPath=Param.InputTable(:,1);
104RootFile=Param.InputTable(:,3);
105SubDir=Param.InputTable(:,2);
106NomType=Param.InputTable(:,4);
107FileExt=Param.InputTable(:,5);
108hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
109[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
110if ~isempty(hdisp),delete(hdisp),end
111%%%%%%%%%%%%
112% The cell array filecell is the list of input file names, while
113% filecell{iview,fileindex}:
114%        iview: line in the table corresponding to a given file series
115%        fileindex: file index within  the file series,
116% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j
117% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
118%%%%%%%%%%%%
119NbView=numel(i1_series);%number of input file series (lines in InputTable)
120NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
121NbField_i=size(i1_series{1},2); %nb of fields for the i index
122NbField=NbField_j*NbField_i; %total number of fields
123
124%% define the directory for result file (with path=RootPath{1})
125OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
126
127%% calibration data and timing: read the ImaDoc files
128[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
129if size(time,1)>1
130    diff_time=max(max(diff(time)));
131    if diff_time>0
132        disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun)
133    end
134end
135if ~isempty(errormsg)
136    disp_uvmat('WARNING',errormsg,checkrun)
137end
138time=mean(time,1); %averaged time taken for the merged field
139if isfield(XmlData{1},'GeometryCalib')
140    tsaiA=XmlData{1}.GeometryCalib;
141else
142    disp_uvmat('ERROR','no geometric calibration available for image A',checkrun)
143    return
144end
145if isfield(XmlData{2},'GeometryCalib')
146    tsaiB=XmlData{2}.GeometryCalib;
147else
148    disp_uvmat('ERROR','no geometric calibration available for image B',checkrun)
149    return
150end
151[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
152
153%% grid of physical positions (given by projection plane)
154if ~Param.CheckObject
155    disp_uvmat('ERROR','a projection plane with interpolation is needed',checkrun)
156    return
157end
158ObjectData=Param.ProjObject;
159xI=ObjectData.RangeX(1):ObjectData.DX:ObjectData.RangeX(2);
160yI=ObjectData.RangeY(1):ObjectData.DY:ObjectData.RangeY(2);
161[XI,YI]=meshgrid(xI,yI);
162U=zeros(size(XI,1),size(XI,2));
163V=zeros(size(XI,1),size(XI,2));
164W=zeros(size(XI,1),size(XI,2));
165
166%% MAIN LOOP ON FIELDS
167warning off
168
169CheckOverwrite=1;%default
170if isfield(Param,'CheckOverwrite')
171    CheckOverwrite=Param.CheckOverwrite;
172end
173
174for index=1:NbField
175   
176    %% generating the name of the merged field
177    i1=i1_series{1}(index);
178    if ~isempty(i2_series{end})
179        i2=i2_series{end}(index);
180    else
181        i2=i1;
182    end
183    j1=1;
184    j2=1;
185    if ~isempty(j1_series{1})
186        j1=j1_series{1}(index);
187        if ~isempty(j2_series{end})
188            j2=j2_series{end}(index);
189        else
190            j2=j1;
191        end
192    end
193    OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},'.nc','_1-2',i1,i2,j1,j2);
194   
195    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
196        disp('program stopped by user')
197        return
198    end
199   
200    if (~CheckOverwrite && exist(OutputFile,'file'))
201        disp('existing output file already exists, skip to next field')
202        continue% skip iteration if the mode overwrite is desactivated and the result file already exists
203    end
204   
205    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
206    Data=cell(1,NbView);%initiate the set Data
207    timeread=zeros(1,NbView);
208   
209    %get Xphys,Yphys,Zphys from 1 or 2 stereo folders. Positions are taken
210    %at the middle between to time step
211    clear ZItemp
212    ZItemp=zeros(size(XI,1),size(XI,2),2);
213    CheckZ=0;
214   
215    if index==1
216        first_img=i1_series{1,1}(1,1); %id of the first image of the series
217    end
218   
219    idtemp=0;
220    for indextemp=index:index+1
221        idtemp=idtemp+1;
222        if NbView==3 % if there is only 1 stereo folder, extract directly Xphys,Yphys and Zphys
223           
224            [Data{3},tild,errormsg] = nc2struct([Param.InputTable{3,1},'/',Param.InputTable{3,2},'/',Param.InputTable{3,3},'_',int2str(first_img+indextemp-1),'.nc']);
225           
226            if  exist('Data{3}.Civ3_FF','var') % FF is present, remove wrong vector
227                temp=find(Data{3}.Civ3_FF==0);
228                Zphys=Data{3}.Zphys(temp);
229                Yphys=Data{3}.Yphys(temp);
230                Xphys=Data{3}.Xphys(temp);
231            else
232                Zphys=Data{3}.Zphys;
233                Yphys=Data{3}.Yphys;
234                Xphys=Data{3}.Xphys;
235            end
236           
237        elseif NbView==4 % is there is 2 stereo folders, get global U and V and compute Zphys
238           
239            %test if the seconde camera is the same for both folder
240            for i=3:4
241                indpt(i)=strfind(Param.InputTable{i,2},'.'); % indice of the "." is the folder name 1
242                indline(i)=strfind(Param.InputTable{i,2},'-'); % indice of the "-" is the folder name1
243                camname{i}=Param.InputTable{i,2}(indline(i)+1:indpt(i)-1);% extract the second camera name
244            end
245           
246            if strcmp(camname{3},camname{4})==0
247                disp_uvmat('ERROR','The 2 stereo folders should have the same camera for the second position',checkrun)
248                return
249            end
250           
251            [Data{3},tild,errormsg] = nc2struct([Param.InputTable{3,1},'/',Param.InputTable{3,2},'/',Param.InputTable{3,3},'_',int2str(first_img+indextemp-1),'.nc']);
252           
253            if exist('Data{3}.Civ3_FF','var') % if FF is present, remove wrong vector
254                temp=find(Data{3}.Civ3_FF==0);
255                Xmid3=Data{3}.Xmid(temp);
256                Ymid3=Data{3}.Ymid(temp);
257                U3=Data{3}.Uphys(temp);
258                V3=Data{3}.Vphys(temp);
259            else
260                Xmid3=Data{3}.Xmid;
261                Ymid3=Data{3}.Ymid;
262                U3=Data{3}.Uphys;
263                V3=Data{3}.Vphys;
264            end
265            %temporary gridd of merging the 2 stereos datas
266            [xq,yq] = meshgrid(min(Xmid3+(U3)/2):(max(Xmid3+(U3)/2)-min(Xmid3+(U3)/2))/128:max(Xmid3+(U3)/2),min(Ymid3+(V3)/2):(max(Ymid3+(V3)/2)-min(Ymid3+(V3)/2))/128:max(Ymid3+(V3)/2));
267           
268            %1st folder : interpolate the first camera (Dalsa1) points on the second (common) camera
269            %(Dalsa 3)
270            x3Q=griddata(Xmid3+(U3)/2,Ymid3+(V3)/2,Xmid3-(U3)/2,xq,yq);
271            y3Q=griddata(Xmid3+(U3)/2,Ymid3+(V3)/2,Ymid3-(V3)/2,xq,yq);
272           
273            [Data{4},tild,errormsg] = nc2struct([Param.InputTable{4,1},'/',Param.InputTable{4,2},'/',Param.InputTable{4,3},'_',int2str(first_img+indextemp-1),'.nc']);
274            if exist('Data{4}.Civ3_FF','var') % if FF is present, remove wrong vector
275                temp=find(Data{4}.Civ3_FF==0);
276                Xmid4=Data{4}.Xmid(temp);
277                Ymid4=Data{4}.Ymid(temp);
278                U4=Data{4}.Uphys(temp);
279                V4=Data{4}.Vphys(temp);
280            else
281                Xmid4=Data{4}.Xmid;
282                Ymid4=Data{4}.Ymid;
283                U4=Data{4}.Uphys;
284                V4=Data{4}.Vphys;
285            end
286           
287            %2nd folder :interpolate the first camera (Dalsa2) points on the second (common) camera
288            %(Dalsa 3)
289            x4Q=griddata(Xmid4+(U4)/2,Ymid4+(V4)/2,Xmid4-(U4)/2,xq,yq);
290            y4Q=griddata(Xmid4+(U4)/2,Ymid4+(V4)/2,Ymid4-(V4)/2,xq,yq);
291           
292            xmid=reshape((x4Q+x3Q)/2,length(xq(:,1)).*length(xq(1,:)),1);
293            ymid=reshape((y4Q+y3Q)/2,length(yq(:,1)).*length(yq(1,:)),1);
294            u=reshape(x4Q-x3Q,length(xq(:,1)).*length(xq(1,:)),1);
295            v=reshape(y4Q-y3Q,length(yq(:,1)).*length(yq(1,:)),1);
296           
297           
298            [Zphys,Xphys,Yphys,error]=shift2z(xmid, ymid, u, v,XmlData); %get Xphy,Yphy and Zphys
299            %remove NaN
300            tempNaN=isnan(Zphys);tempind=find(tempNaN==1);
301            Zphys(tempind)=[];
302            Xphys(tempind)=[];
303            Yphys(tempind)=[];       
304        end
305       
306        if NbView>2
307            ZItemp(:,:,idtemp)=griddata(Xphys,Yphys,Zphys,XI,YI); %interpolation on the choosen gridd
308            CheckZ=1;
309        end     
310    end
311    ZI=mean(ZItemp,3); %mean between the two time step
312   
313    [Xa,Ya]=px_XYZ(XmlData{1}.GeometryCalib,[],XI,YI,ZI);% set of image coordinates on view a
314    [Xb,Yb]=px_XYZ(XmlData{2}.GeometryCalib,[],XI,YI,ZI);% set of image coordinates on view b
315   
316   
317    for iview=1:2
318        %% reading input file(s)
319        [Data{iview},tild,errormsg]=read_civdata(filecell{iview,index},{'vec(U,V)'},'*');
320        if ~isempty(errormsg)
321            disp_uvmat('ERROR',['ERROR in civ2vel_3C/read_field/' errormsg],checkrun)
322            return
323        end
324        % get the time defined in the current file if not already defined from the xml file
325        if isfield(Data{iview},'Time')&& (Data{iview}.Time-Data{1}.Time)<0.0001
326            Time=Data{iview}.Time;
327        else
328            disp_uvmat('ERROR','Time undefined or not synchronous',checkrun)
329            return
330        end
331        if isfield(Data{iview},'Dt')&& isequal(Data{iview}.Dt,Data{1}.Dt)
332            Dt=Data{iview}.Dt;
333        else
334            disp_uvmat('ERROR','Dt undefined or not synchronous',checkrun)
335            return
336        end
337    end
338    %remove wrong vector
339    if isfield(Data{1},'FF')
340        temp=find(Data{1}.FF==0);
341        X1=Data{1}.X(temp);
342        Y1=Data{1}.Y(temp);
343        U1=Data{1}.U(temp);
344        V1=Data{1}.V(temp);
345    else
346        X1=Data{1}.X;
347        Y1=Data{1}.Y;
348        U1=Data{1}.U;
349        V1=Data{1}.V;
350    end
351    Ua=griddata(X1,Y1,U1,Xa,Ya);
352    Va=griddata(X1,Y1,V1,Xa,Ya);
353    [Ua,Va,Xa,Ya]=Ud2U(XmlData{1}.GeometryCalib,Xa,Ya,Ua,Va); % convert Xd data to X
354    [A]=get_coeff(XmlData{1}.GeometryCalib,Xa,Ya,XI,YI,ZI); %get coef A~
355   
356    %remove wrong vector
357    if isfield(Data{2},'FF')
358        temp=find(Data{2}.FF==0);
359        X2=Data{2}.X(temp);
360        Y2=Data{2}.Y(temp);
361        U2=Data{2}.U(temp);
362        V2=Data{2}.V(temp);
363    else
364        X2=Data{2}.X;
365        Y2=Data{2}.Y;
366        U2=Data{2}.U;
367        V2=Data{2}.V;
368    end
369    Ub=griddata(X2,Y2,U2,Xb,Yb);
370    Vb=griddata(X2,Y2,V2,Xb,Yb);
371    [Ub,Vb,Xb,Yb]=Ud2U(XmlData{2}.GeometryCalib,Xb,Yb,Ub,Vb); % convert Xd data to X
372   
373    [B]=get_coeff(XmlData{2}.GeometryCalib,Xb,Yb,XI,YI,ZI); %get coef B~
374   
375   
376    % System to solve
377    S=ones(size(XI,1),size(XI,2),3);
378    D=ones(size(XI,1),size(XI,2),3,3);
379   
380    S(:,:,1)=A(:,:,1,1).*Ua+A(:,:,2,1).*Va+B(:,:,1,1).*Ub+B(:,:,2,1).*Vb;
381    S(:,:,2)=A(:,:,1,2).*Ua+A(:,:,2,2).*Va+B(:,:,1,2).*Ub+B(:,:,2,2).*Vb;
382    S(:,:,3)=A(:,:,1,3).*Ua+A(:,:,2,3).*Va+B(:,:,1,3).*Ub+B(:,:,2,3).*Vb;
383    D(:,:,1,1)=A(:,:,1,1).*A(:,:,1,1)+A(:,:,2,1).*A(:,:,2,1)+B(:,:,1,1).*B(:,:,1,1)+B(:,:,2,1).*B(:,:,2,1);
384    D(:,:,1,2)=A(:,:,1,1).*A(:,:,1,2)+A(:,:,2,1).*A(:,:,2,2)+B(:,:,1,1).*B(:,:,1,2)+B(:,:,2,1).*B(:,:,2,2);
385    D(:,:,1,3)=A(:,:,1,1).*A(:,:,1,3)+A(:,:,2,1).*A(:,:,2,3)+B(:,:,1,1).*B(:,:,1,3)+B(:,:,2,1).*B(:,:,2,3);
386    D(:,:,2,1)=A(:,:,1,2).*A(:,:,1,1)+A(:,:,2,2).*A(:,:,2,1)+B(:,:,1,2).*B(:,:,1,1)+B(:,:,2,2).*B(:,:,2,1);
387    D(:,:,2,2)=A(:,:,1,2).*A(:,:,1,2)+A(:,:,2,2).*A(:,:,2,2)+B(:,:,1,2).*B(:,:,1,2)+B(:,:,2,2).*B(:,:,2,2);
388    D(:,:,2,3)=A(:,:,1,2).*A(:,:,1,3)+A(:,:,2,2).*A(:,:,2,3)+B(:,:,1,2).*B(:,:,1,3)+B(:,:,2,2).*B(:,:,2,3);
389    D(:,:,3,1)=A(:,:,1,3).*A(:,:,1,1)+A(:,:,2,3).*A(:,:,2,1)+B(:,:,1,3).*B(:,:,1,1)+B(:,:,2,3).*B(:,:,2,1);
390    D(:,:,3,2)=A(:,:,1,3).*A(:,:,1,2)+A(:,:,2,3).*A(:,:,2,2)+B(:,:,1,3).*B(:,:,1,2)+B(:,:,2,3).*B(:,:,2,2);
391    D(:,:,3,3)=A(:,:,1,3).*A(:,:,1,3)+A(:,:,2,3).*A(:,:,2,3)+B(:,:,1,3).*B(:,:,1,3)+B(:,:,2,3).*B(:,:,2,3);
392    for indj=1:size(XI,1)
393        for indi=1:size(XI,2)
394            dxyz=(squeeze(D(indj,indi,:,:))*1000)\(squeeze(S(indj,indi,:))*1000); % solving...
395            U(indj,indi)=dxyz(1);
396            V(indj,indi)=dxyz(2);
397            W(indj,indi)=dxyz(3);
398        end
399    end
400    Error=zeros(size(XI,1),size(XI,2),4);
401    Error(:,:,1)=A(:,:,1,1).*U+A(:,:,1,2).*V+A(:,:,1,3).*W-Ua;
402    Error(:,:,2)=A(:,:,2,1).*U+A(:,:,2,2).*V+A(:,:,2,3).*W-Va;
403    Error(:,:,3)=B(:,:,1,1).*U+B(:,:,1,2).*V+B(:,:,1,3).*W-Ub;
404    Error(:,:,4)=B(:,:,2,1).*U+B(:,:,2,2).*V+B(:,:,2,3).*W-Vb;
405   
406   
407    %% recording the merged field
408    if index==1% initiate the structure at first index
409        MergeData.ListGlobalAttribute={'Conventions','Time','Dt','CoordUnit'};
410        MergeData.Conventions='uvmat';
411        if isfield (XmlData{1}.GeometryCalib,'CoordUnit') && isfield (XmlData{2}.GeometryCalib,'CoordUnit') && strcmp(XmlData{1}.GeometryCalib.CoordUnit, XmlData{2}.GeometryCalib.CoordUnit)
412        MergeData.CoordUnit=XmlData{1}.GeometryCalib.CoordUnit;
413        else
414            disp_uvmat('ERROR','inconsistent coord units in the two input velocity series',checkrun)
415            return
416        end
417        MergeData.ListVarName={'coord_x','coord_y','U','V','W','Error'};
418        MergeData.VarDimName={'coord_x','coord_y',{'coord_y','coord_x'},{'coord_y','coord_x'}...
419            {'coord_y','coord_x'},{'coord_y','coord_x'}};
420        MergeData.VarAttribute{6}.unit='pixel'; %error estimate expressed in pixel
421        if CheckZ
422            MergeData.ListVarName=[MergeData.ListVarName {'Z'}];
423            MergeData.VarDimName=[MergeData.ListVarName {'coord_y','coord_x'}];
424            MergeData.Z=ZI;
425        end
426        MergeData.coord_x=xI;
427        MergeData.coord_y=yI;
428    end
429    MergeData.Time=Time;
430    MergeData.Dt=Dt;
431    MergeData.U=U/Dt;
432    MergeData.V=V/Dt;
433    MergeData.W=W/Dt;
434   
435   
436    mfx=(XmlData{1}.GeometryCalib.fx_fy(1)+XmlData{2}.GeometryCalib.fx_fy(1))/2;
437    mfy=(XmlData{1}.GeometryCalib.fx_fy(2)+XmlData{2}.GeometryCalib.fx_fy(2))/2;
438    MergeData.Error=0.25*(mfx+mfy)*sqrt(sum(Error.^2,3));
439    errormsg=struct2nc(OutputFile,MergeData);%save result file
440    if isempty(errormsg)
441        disp(['output file ' OutputFile ' written'])
442    else
443        disp(errormsg)
444    end
445end
446
447
448function [A]=get_coeff(Calib,X,Y,x,y,z) % compute A~ coefficients
449R=(Calib.R)';%rotation matrix
450T_z=Calib.Tx_Ty_Tz(3);
451T=R(7)*x+R(8)*y+R(9)*z+T_z;
452
453A(:,:,1,1)=(R(1)-R(7)*X)./T;
454A(:,:,1,2)=(R(2)-R(8)*X)./T;
455A(:,:,1,3)=(R(3)-R(9)*X)./T;
456A(:,:,2,1)=(R(4)-R(7)*Y)./T;
457A(:,:,2,2)=(R(5)-R(8)*Y)./T;
458A(:,:,2,3)=(R(6)-R(9)*Y)./T;
459
460function [U,V,X,Y]=Ud2U(Calib,Xd,Yd,Ud,Vd) % convert Xd to X  and Ud to U
461
462X1d=Xd-Ud/2;
463X2d=Xd+Ud/2;
464Y1d=Yd-Vd/2;
465Y2d=Yd+Vd/2;
466
467X1=(X1d-Calib.Cx_Cy(1))./Calib.fx_fy(1).*(1 + Calib.kc.*Calib.fx_fy(1).^(-2).*(X1d-Calib.Cx_Cy(1)).^2 + Calib.kc.*Calib.fx_fy(2).^(-2).*(Y1d-Calib.Cx_Cy(2)).^2 ).^(-1);
468X2=(X2d-Calib.Cx_Cy(1))./Calib.fx_fy(1).*(1 + Calib.kc.*Calib.fx_fy(1).^(-2).*(X2d-Calib.Cx_Cy(1)).^2 + Calib.kc.*Calib.fx_fy(2).^(-2).*(Y2d-Calib.Cx_Cy(2)).^2 ).^(-1);
469Y1=(Y1d-Calib.Cx_Cy(2))./Calib.fx_fy(2).*(1 + Calib.kc.*Calib.fx_fy(1).^(-2).*(X1d-Calib.Cx_Cy(1)).^2 + Calib.kc.*Calib.fx_fy(2).^(-2).*(Y1d-Calib.Cx_Cy(2)).^2 ).^(-1);
470Y2=(Y2d-Calib.Cx_Cy(2))./Calib.fx_fy(2).*(1 + Calib.kc.*Calib.fx_fy(1).^(-2).*(X2d-Calib.Cx_Cy(1)).^2 + Calib.kc.*Calib.fx_fy(2).^(-2).*(Y2d-Calib.Cx_Cy(2)).^2 ).^(-1);
471
472U=X2-X1;
473V=Y2-Y1;
474X=X1+U/2;
475Y=Y1+V/2;
476
477
478
479function [z,Xphy,Yphy,error]=shift2z(xmid, ymid, u, v,XmlData) % get H from stereo data
480z=0;
481error=0;
482
483
484%% first image
485Calib_A=XmlData{1}.GeometryCalib;
486R=(Calib_A.R)';
487x_a=xmid- u/2;
488y_a=ymid- v/2;
489z_a=R(7)*x_a+R(8)*y_a+Calib_A.Tx_Ty_Tz(1,3);
490Xa=(R(1)*x_a+R(2)*y_a+Calib_A.Tx_Ty_Tz(1,1))./z_a;
491Ya=(R(4)*x_a+R(5)*y_a+Calib_A.Tx_Ty_Tz(1,2))./z_a;
492
493A_1_1=R(1)-R(7)*Xa;
494A_1_2=R(2)-R(8)*Xa;
495A_1_3=R(3)-R(9)*Xa;
496A_2_1=R(4)-R(7)*Ya;
497A_2_2=R(5)-R(8)*Ya;
498A_2_3=R(6)-R(9)*Ya;
499Det=A_1_1.*A_2_2-A_1_2.*A_2_1;
500Dxa=(A_1_2.*A_2_3-A_2_2.*A_1_3)./Det;
501Dya=(A_2_1.*A_1_3-A_1_1.*A_2_3)./Det;
502
503%% second image
504%loading shift angle
505
506Calib_B=XmlData{2}.GeometryCalib;
507R=(Calib_B.R)';
508
509
510x_b=xmid+ u/2;
511y_b=ymid+ v/2;
512z_b=R(7)*x_b+R(8)*y_b+Calib_B.Tx_Ty_Tz(1,3);
513Xb=(R(1)*x_b+R(2)*y_b+Calib_B.Tx_Ty_Tz(1,1))./z_b;
514Yb=(R(4)*x_b+R(5)*y_b+Calib_B.Tx_Ty_Tz(1,2))./z_b;
515B_1_1=R(1)-R(7)*Xb;
516B_1_2=R(2)-R(8)*Xb;
517B_1_3=R(3)-R(9)*Xb;
518B_2_1=R(4)-R(7)*Yb;
519B_2_2=R(5)-R(8)*Yb;
520B_2_3=R(6)-R(9)*Yb;
521Det=B_1_1.*B_2_2-B_1_2.*B_2_1;
522Dxb=(B_1_2.*B_2_3-B_2_2.*B_1_3)./Det;
523Dyb=(B_2_1.*B_1_3-B_1_1.*B_2_3)./Det;
524
525%% result
526Den=(Dxb-Dxa).*(Dxb-Dxa)+(Dyb-Dya).*(Dyb-Dya);
527error=abs(((Dyb-Dya).*(-u)-(Dxb-Dxa).*(-v)))./Den;
528% ex=-error.*(Dyb-Dya);
529% ey=-error.*(Dxb-Dxa);
530
531% z1=-u./(Dxb-Dxa);
532% z2=-v./(Dyb-Dya);
533z=((Dxb-Dxa).*(-u)+(Dyb-Dya).*(-v))./Den;
534
535xnew(1,:)=Dxa.*z+x_a;
536xnew(2,:)=Dxb.*z+x_b;
537ynew(1,:)=Dya.*z+y_a;
538ynew(2,:)=Dyb.*z+y_b;
539Xphy=mean(xnew,1);
540Yphy=mean(ynew,1);
541
542
543
544
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